Plot heatmap of sample level counts in logcpm

Source: R/relabu_heatmap.R

Plot heatmap of sample level counts in logcpm

relabu_heatmap(
  MAE,
  tax_level,
  sort_by = c("nosort", "conditions", "organisms", "alphabetically"),
  sample_conditions = c(),
  isolate_organisms = c(),
  isolate_samples = c(),
  discard_samples = c(),
  log_cpm = TRUE
)

Arguments

MAE

A multi-assay experiment object

tax_level

The taxon level used for organisms

sort_by

Sort bars by one of c('nosort', 'conditions', 'organisms', 'alphabetically')

sample_conditions

Plot conditions e.g. c('SEX', 'AGE')

isolate_organisms

Isolate specific organisms e.g. c('Hepacivirus')

isolate_samples

Isolate specific samples e.g. c('SAM_01', 'SAM_02')

discard_samples

Discard specific samples e.g. c('SAM_01', 'SAM_02')

log_cpm

Convert counts to logcpm

Value

A plotly object

Examples

data_dir <- system.file("extdata/MAE.rds", package = "animalcules")
toy_data <- readRDS(data_dir)
p <- relabu_heatmap(toy_data,
  tax_level = "genus",
  sort_by = "conditions",
  sample_conditions = c("SEX", "AGE")
)
p